For the post format compat code this isn't an issue since it's scheduled at an earlier priority (7) and do_shortcode then picks that up at priority 11 at the_content. That's why you can't reproduce this in Twenty Twelve.

The structured code, however, doesn't run do_shortcode and relies on autoembed for external links which can in fact produce a shortcode since audio and video are registered embed handlers. Running the result from autoembed through shortcodes again should do the trick. See 24235.diff​.